Place guajillo peppers in a saucepan, cover with water, and boil until softened, about 10 minutes. Drain.
Combine lime juice, 2 cloves garlic, cumin, and cloves in a small saucepan over medium heat; bring to a boil. Remove from heat and cool for 5 minutes. Pour into a blender, add guajillo peppers, and blend until smooth. Add 1 to 2 tablespoons of the water if the sauce is too thick.
Heat oil in a large saucepan over medium heat and cook onion slices until soft and translucent, about 5 minutes. Stir in vegetable protein; cook and stir for 2 minutes. Pour in guajillo sauce and remaining water; season with salt. Bring to a boil; reduce heat to medium-low cook, covered, until flavors combine, about 10 minutes.
Set oven rack about 6 inches from the heat source and preheat the oven's broiler. Combine tomatoes and chile de arbol peppers in a baking dish.
Roast tomatoes and peppers until charred, 5 to 10 minutes. Cool tomatoes slightly. Peel.
Combine peeled tomatoes, peppers, 1 slice onion, 1 clove garlic, and salt in a blender; blend until smooth. Pour salsa into a small bowl.
Warm corn tortillas in a skillet. Divide vegetable protein mixture amongst tortillas and top with salsa, chopped onion, and cilantro.